+Open data
-Basic information
Entry | Database: PDB / ID: 5ysi | ||||||
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Title | SdeA mART-C domain EE/AA NCA complex | ||||||
Components | Ubiquitinating/deubiquitinating enzyme SdeA | ||||||
Keywords | HYDROLASE / SdeA / E3 ligase / Legionella | ||||||
Function / homology | Function and homology information NAD+-protein-arginine ADP-ribosyltransferase / deNEDDylase activity / NAD+-protein-arginine ADP-ribosyltransferase activity / protein deneddylation / Transferases; Acyltransferases; Aminoacyltransferases / K63-linked deubiquitinase activity / protein deubiquitination / cysteine-type peptidase activity / host cell / nucleotidyltransferase activity ...NAD+-protein-arginine ADP-ribosyltransferase / deNEDDylase activity / NAD+-protein-arginine ADP-ribosyltransferase activity / protein deneddylation / Transferases; Acyltransferases; Aminoacyltransferases / K63-linked deubiquitinase activity / protein deubiquitination / cysteine-type peptidase activity / host cell / nucleotidyltransferase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / protein ubiquitination / nucleotide binding / proteolysis / extracellular region Similarity search - Function | ||||||
Biological species | Legionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.546 Å | ||||||
Authors | Kim, L. / Kwon, D.H. / Song, H.K. | ||||||
Citation | Journal: J. Mol. Biol. / Year: 2018 Title: Structural and Biochemical Study of the Mono-ADP-Ribosyltransferase Domain of SdeA, a Ubiquitylating/Deubiquitylating Enzyme from Legionella pneumophila Authors: Kim, L. / Kwon, D.H. / Kim, B.H. / Kim, J. / Park, M.R. / Park, Z.Y. / Song, H.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ysi.cif.gz | 63.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ysi.ent.gz | 51.1 KB | Display | PDB format |
PDBx/mmJSON format | 5ysi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ys/5ysi ftp://data.pdbj.org/pub/pdb/validation_reports/ys/5ysi | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 16923.611 Da / Num. of mol.: 1 / Fragment: UNP residues 761-960 / Mutation: E860A, E862A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Legionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria) Strain: Philadelphia 1 / Gene: sdeA / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: Q6RCR0, UniProt: Q5ZTK4*PLUS, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases, Transferases; Acyltransferases; Aminoacyltransferases, NAD+-protein- ...References: UniProt: Q6RCR0, UniProt: Q5ZTK4*PLUS, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases, Transferases; Acyltransferases; Aminoacyltransferases, NAD+-protein-arginine ADP-ribosyltransferase |
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#2: Chemical | ChemComp-NCA / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.78 Å3/Da / Density % sol: 30.93 % Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS. |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG400, Tris |
-Data collection
Diffraction | Mean temperature: 193 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: May 5, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.546→34.555 Å / Num. obs: 36284 / % possible obs: 99.56 % / Redundancy: 6.7 % / Net I/σ(I): 32.37 |
Reflection shell | Resolution: 1.546→1.602 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.542 / Num. unique obs: 1754 / % possible all: 97.33 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.546→34.555 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 24.65
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.546→34.555 Å
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Refine LS restraints |
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LS refinement shell |
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